DESCRIPTION

The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object.

This module has been developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions.

This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See Bio::SeqAnalysisParserI.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp, Mark Fiers

Email hlapp@gmx.net m.w.e.j.fiers@plant.wag-ur.nl

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

analysis_method

next_feature

Title : next_feature
Usage : while($gene = $Genemark->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Genemark result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :

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